[Cdd-commits] r1065 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Sep  8 11:16:52 2008
New Revision: 1065

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added dotur


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Sep  8 11:16:52 2008
@@ -2115,7 +2115,7 @@
 
 Depends: coalesce
 Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
-License: to be clarified
+License: not specified
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
 Pkg-Description: outdated program to estimate population-genetic parameters
@@ -2136,6 +2136,7 @@
 
 Depends: lamarc
 Homepage: http://evolution.gs.washington.edu/lamarc/
+License: Apache V2.0
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
 Pkg-Description: estimate population-genetic parameters
@@ -2151,3 +2152,56 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Comment: BioLinux contains a dendroscope package which is available
+ at http://www.dendroscope.org but this project has only a
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: dotter
+Homepage: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detailed comparison of two sequences
+ Dotter is a graphical dotplot program for detailed comparison of two
+ sequences.  Here, every residue in one sequence is compared to every
+ residue in the other sequence. The first sequence runs along the
+ x-axis and the second sequence along the y-axis. In regions where the
+ two sequences are similar to each other, a row of high scores will
+ run diagonally across the dot matrix. If you're comparing a sequence
+ against itself to find internal repeats, you'll notice that the main
+ diagonal scores maximally, since it's the 100% perfect self-match.
+ .
+ To make the score matrix more intelligible, the pairwise scores are
+ averaged over a sliding window which runs diagonally. The averaged
+ score matrix forms a three-dimensional landscape, with the two
+ sequences in two dimensions and the height of the peaks in the
+ third. This landscape is projected onto two dimensions by aid of
+ greyscales - the darker grey of a peak, the higher it is.
+ .
+ Dotter provides a tool to explore the visual appearance of this
+ landscape, as well as a tool to examine the sequence alignment it
+ represents.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+Comment: Homepage is currently unavailable but the source might be
+ obtainable from freebsd.org.
+
+Depends: dotur
+Homepage: http://schloss.micro.umass.edu/software/dotur.html
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Defining Operational Taxonomic Units and estimating species Richness
+ Dotur (Distance Based OTU and Richness determination) is a computer
+ program that takes a distance matrix describing the genetic distance
+ between DNA sequence data and assigns sequences to operational
+ taxonomic units (OTUs) using either the furthest, average, or nearest
+ neighbor algorithms for all possible distances that can be described
+ using the distance matrix.  Using the OTU composition data, dotur
+ constructs collector's and rarefaction curves for sampling intensity,
+ richness estimators, and diversity indices.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html